MeshlabAuto with PyMOL

Automation of Meshlab and PyMOL.

Overview

Meshlab is an open source, portable, and extensible system for the processing and editing of unstructured 3D triangular meshes. PyMOL is a paid-for or open source molecular visualisation program. See TheNerdJedi's original repo for an introduction to automating MeshLab. This fork extends the functionality of MeshLabAuto by including a template for the automated extraction of 3D meshes from PyMOL, which can then be fed into scripts based on the original MeshLabAuto code.

Automating PyMOl mesh extraction

PyMOL can export 3D models in a range of formats, but the .wrl format carries colour information that is useful for further rendering. Therefore, .pml scripts can be used to extract many 3D models from PyMOL in quick succession.You can place lumps of Python code within Python code blocks:

python
readme_string = "Meshlab can work with {}"
print(readme_string.format("PyMOL!"))
python end

Alternatively, my approach utilitsed PyMOL's exec() command to combine string interpolation and for loops for the export of multiple 3D models.

Example .pml file for outputting 3D meshes

load my-simulation_aligned.pdb # A .pdb file containing individual 'frames' of a molecular simulation.

set_view (\
     0.534421325,   -0.815990210,   -0.220345959,\
    -0.482305050,   -0.080326393,   -0.872313380,\
     0.694099009,    0.572455585,   -0.436485291,\
     0.000010939,    0.000004098,  -58.172981262,\
     48.423061371,   52.551383972,    6.932424545,\
    -164.967880249,  281.294006348,  -20.000000000 )  # The viewport we want to see our molecule from.

mystr1 = "my-simulation_aligned_000{}"
mystr2 = "anim_{}.wrl"

# Now we have three for loops which carry out the selection/editing of components of our model for each 'frame':

exec("for i in range(1, 10): cmd.disable('all'); cmd.enable(mystr1.format(i)); cmd.select('obj',mystr1.format(i)); cmd.select('obj2',mystr1.format(i)); cmd.select('obj_linker','resn Lys & obj & !(obj & bto name N + bto name C + name HA)'); cmd.select('obj_backbone','obj & !obj_linker'); cmd.color('green','obj_backbone'); cmd.color('yellow','obj_linker'); util.cnc('obj'); cmd.show('sticks','obj'); cmd.show('cartoon','obj'); print(i); cmd.delete('contacts'); cmd.distance('contacts','obj','obj2',3.6,2); cmd.enable('contacts'); cmd.hide('labels'); cmd.hide('everything','elem H'); cmd.set('dash_width', 2.5); cmd.show('sticks', '!elem H'); cmd.show('cartoon'); cmd.show('spheres', '!elem H'); cmd.show('dashes'); cmd.set('sphere_scale', 0.2); cmd.save(mystr2.format(i));")
mystr1 = "my-simulation_aligned_00{}"
exec("for i in range(11, 100): cmd.disable('all'); cmd.enable(mystr1.format(i)); cmd.select('obj',mystr1.format(i)); cmd.select('obj2',mystr1.format(i)); cmd.select('obj_linker','resn Lys & obj & !(obj & bto name N + bto name C + name HA)'); cmd.select('obj_backbone','obj & !obj_linker'); cmd.color('green','obj_backbone'); cmd.color('yellow','obj_linker'); util.cnc('obj'); cmd.show('sticks','obj'); cmd.show('cartoon','obj'); print(i); cmd.delete('contacts'); cmd.distance('contacts','obj','obj2',3.6,2); cmd.enable('contacts'); cmd.hide('labels'); cmd.hide('everything','elem H'); cmd.set('dash_width', 2.5); cmd.show('sticks', '!elem H'); cmd.show('cartoon'); cmd.show('spheres', '!elem H'); cmd.show('dashes'); cmd.set('sphere_scale', 0.2); cmd.save(mystr2.format(i));")
mystr1 = "my-simulation_aligned_0{}"
exec("for i in range(100, 101): cmd.disable('all'); cmd.enable(mystr1.format(i)); cmd.select('obj',mystr1.format(i)); cmd.select('obj2',mystr1.format(i)); cmd.select('obj_linker','resn Lys & obj & !(obj & bto name N + bto name C + name HA)'); cmd.select('obj_backbone','obj & !obj_linker'); cmd.color('green','obj_backbone'); cmd.color('yellow','obj_linker'); util.cnc('obj'); cmd.show('sticks','obj'); cmd.show('cartoon','obj'); print(i); cmd.delete('contacts'); cmd.distance('contacts','obj','obj2',3.6,2); cmd.enable('contacts'); cmd.hide('labels'); cmd.hide('everything','elem H'); cmd.set('dash_width', 2.5); cmd.show('sticks', '!elem H'); cmd.show('cartoon'); cmd.show('spheres', '!elem H'); cmd.show('dashes'); cmd.set('sphere_scale', 0.2); cmd.save(mystr2.format(i));")

This outputs 100 frames of animation of a molecule. When imported into the correct software, animations such as these are made possible.